MuPlex: multi-objective multiplex PCR assay design
We have developed a web-enabled system called MuPlex that aids researchers in the design of multiplex PCR assays. Multiplex PCR is a key technology for an endless list of applications, including detecting infectious microorganisms, whole-genome sequencing and closure, forensic analysis and for enabling flexible yet low-cost genotyping. However, the design of a multiplex PCR assays is computationally challenging because it involves tradeoffs among competing objectives, and extensive computational analysis is required in order to screen out primer-pair cross interactions. With MuPlex, users specify a set of DNA sequences along with primer selection criteria, interaction parameters and the target multiplexing level. MuPlex designs a set of multiplex PCR assays designed to cover as many of the input sequences as possible. MuPlex provides multiple solution alternatives that reveal tradeoffs among competing objectives. MuPlex is uniquely designed for large-scale multiplex PCR assay design in an automated high-throughput environment, where high coverage of potentially thousands of single nucleotide polymorphisms is required. The server is available at http://genomics14.bu.edu:8080/MuPlex/MuPlex.html.
Multiplex Polymerase Chain Reaction (PCR) assay is to amplify multiple target DNAs simultaneously using different primer pairs for each target DNA. Recently, it is widely used for various biology applications such as genotyping. For sucessful experiments, both the primer pairs for each target DNA and grouping of targets to be actually amplified in one tube should be optimized. This involves mul...متن کامل
Simultaneous Detection of Integrase and Antibiotic Resistance Genes within SXT Constin in Vibrio cholerae O1 El Tor Strains Isolated from Iran Using Multiplex-PCR
Objective(s) Amongst the various antibiotic resistant elements in Vibrio. cholerae, SXT constin (SXT-C) is important. We were going to design a quick method for determination of antibiotic resistance gene pattern in SXT-C. Materials and Methods Ninety four V. cholerae O1El Tor isolates were used in this study. Antibiotic susceptibility testing, multiplex PCR amplification of SXT-C containing...متن کامل
Validation of a diagnostic multiplex polymerase chain reaction assay for infectious posterior uveitis.
OBJECTIVE To validate a multiplex polymerase chain reaction (PCR) assay capable of simultaneously screening vitreous biopsy specimens for a panel of common pathogens in posterior uveitis. METHODS A multiplex PCR assay using novel primer sets for cytomegalovirus (CMV), herpes simplex virus (HSV), varicella zoster virus (VZV), and Toxoplasma gondii was developed. The sensitivity of the assay wa...متن کامل
Evaluation of a multiplex polymerase chain reaction assay for simultaneous detection of Rhodococcus equi and the vapA gene.
OBJECTIVE To evaluate sensitivity and specificity of a multiplex polymerase chain reaction (PCR) assay for simultaneous detection of Rhodococcus equi and differentiation of strains that contain the virulence-associated gene (vapA) from strains that do not. SAMPLE POPULATION 187 isolates of R equi from equine and nonequine tissue and environmental specimens and 27 isolates of bacterial species...متن کامل
Background: Yersinia pestis and Francisella tularensis cause plague and tularemia, which are known as diseases of the newborn and elderly, respectively. Immunological and culture-based detection methods of these bacteria are time-consuming, costly, complicated and require advanced equipment. We aimed to design and synthesize a gene structure as positive control for molecular detection of these ...متن کامل